Academic Journal
PIF - A Java library for finding atomic interactions and extracting geometric features supporting the analysis of protein structures.
| Τίτλος: | PIF - A Java library for finding atomic interactions and extracting geometric features supporting the analysis of protein structures. |
|---|---|
| Συγγραφείς: | Jargieło W; Silesian University of Technology, Department of Applied Informatics, Akademicka 16, Gliwice 44-100, Poland., Małysiak-Mrozek B; Silesian University of Technology, Department of Distributed Systems and Informatic Devices, Akademicka 16, Gliwice 44-100, Poland., Mrozek D; Silesian University of Technology, Department of Applied Informatics, Akademicka 16, Gliwice 44-100, Poland. |
| Πηγή: | Methods (San Diego, Calif.) [Methods] 2022 Sep; Vol. 205, pp. 63-72. Date of Electronic Publication: 2022 Jun 18. |
| Τύπος έκδοσης: | Journal Article; Research Support, Non-U.S. Gov't |
| Γλώσσα: | English |
| Στοιχεία περιοδικού: | Publisher: Academic Press Country of Publication: United States NLM ID: 9426302 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1095-9130 (Electronic) Linking ISSN: 10462023 NLM ISO Abbreviation: Methods Subsets: MEDLINE |
| Imprint Name(s): | Publication: Duluth, MN : Academic Press Original Publication: San Diego : Academic Press, c1990- |
| Ιατρικοί όροι (MeSH): | Proteins*/chemistry , Artificial Intelligence*, Gene Library |
| Περίληψη: | Proteins play an essential role in the functioning of living organisms. The enormity of the atomic interactions in proteins is essential in controlling their spatial structures and dynamics. It can also provide scientists with valuable information that help to determine the native structures of proteins. This paper presents the PIF (Protein Interaction Finder) library for the Java language, enabling the identification of selected atomic interactions (hydrogen and disulfide bonds, ionic, hydrophobic, aromatic-aromatic, sulfur-aromatic, and amino-aromatic interactions) based on the three-dimensional structure of proteins. The interaction calculation rules applied in PIF rely on documented theoretical foundations gathered from experimental studies of interactions in native protein structures. The library has a universal purpose, supporting drug discovery and development processes and protein structure modeling. Finding the atomic interactions can also deliver numerical features for various Artificial Intelligence (AI) models built for protein analysis. The conducted research comparing the results obtained with the use of the PIF library and competing tools has shown that our solution can effectively determine the interactions occurring in protein structures for entire collections of proteins. Moreover, as a solution that provides a programming interface, the PIF library can be used in any Java project, making it a universal tool. (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.) |
| Contributed Indexing: | Keywords: Atomic interactions; Feature extraction; Java; Library; Proteins |
| Substance Nomenclature: | 0 (Proteins) |
| Entry Date(s): | Date Created: 20220620 Date Completed: 20220825 Latest Revision: 20250728 |
| Update Code: | 20260130 |
| DOI: | 10.1016/j.ymeth.2022.04.018 |
| PMID: | 35724844 |
| Βάση Δεδομένων: | MEDLINE |
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